title: Evaluation of strong cation exchange versus isoelectric focusing of peptides for multidimensional liquid chromatography-tandem mass spectrometry.
abstract: Shotgun proteome analysis platforms based on multidimensional liquid chromatography-tandem mass spectrometry (LC-MS/MS) provide a powerful means to discover biomarker candidates in tissue specimens. Analysis platforms must balance sensitivity for peptide detection, reproducibility of detected peptide inventories and analytical throughput for protein amounts commonly present in tissue biospecimens (< 100 microg), such that platform stability is sufficient to detect modest changes in complex proteomes. We compared shotgun proteomics platforms by analyzing tryptic digests of whole cell and tissue proteomes using strong cation exchange (SCX) and isoelectric focusing (IEF) separations of peptides prior to LC-MS/MS analysis on a LTQ-Orbitrap hybrid instrument. IEF separations provided superior reproducibility and resolution for peptide fractionation from samples corresponding to both large (100 microg) and small (10 microg) protein inputs. SCX generated more peptide and protein identifications than did IEF with small (10 microg) samples, whereas the two platforms yielded similar numbers of identifications with large (100 microg) samples. In nine replicate analyses of tryptic peptides from 50 microg colon adenocarcinoma protein, overlap in protein detection by the two platforms was 77% of all proteins detected by both methods combined. IEF more quickly approached maximal detection, with 90% of IEF-detectable medium abundance proteins (those detected with a total of 3-4 peptides) detected within three replicate analyses. In contrast, the SCX platform required six replicates to detect 90% of SCX-detectable medium abundance proteins. High reproducibility and efficient resolution of IEF peptide separations make the IEF platform superior to the SCX platform for biomarker discovery via shotgun proteomic analyses of tissue specimens.
authors.affiliation: Jim Ayers Institute for Precancer Detection and Diagnosis, Vanderbilt-Ingram Cancer Center, Medical Research Building III, 465 21st Avenue South, Nashville, Tennessee 37232, USA.
authors.forename: Robbert J C
authors.initials: RJ
authors.lastname: Slebos
authors.forename: Jonathan W C
authors.initials: JW
authors.lastname: Brock
authors.forename: Nancy F
authors.initials: NF
authors.lastname: Winters
authors.forename: Sarah R
authors.initials: SR
authors.lastname: Stuart
authors.forename: Misti A
authors.initials: MA
authors.lastname: Martinez
authors.forename: Ming
authors.initials: M
authors.lastname: Li
authors.forename: Mathew C
authors.initials: MC
authors.lastname: Chambers
authors.forename: Lisa J
authors.initials: LJ
authors.lastname: Zimmerman
authors.forename: Amy J
authors.initials: AJ
authors.lastname: Ham
authors.forename: David L
authors.initials: DL
authors.lastname: Tabb
authors.forename: Daniel C
authors.initials: DC
authors.lastname: Liebler
mesh_terms: D000230:Adenocarcinoma / Q000378:metabolism; D015415:Biomarkers / Q000378:metabolism; D002412:Cations; D002852:Chromatography, Ion Exchange / Q000379:methods*; D002853:Chromatography, Liquid / Q000379:methods*; D003110:Colonic Neoplasms / Q000378:metabolism; D019295:Computational Biology / Q000379:methods*; D015972:Gene Expression Regulation, Neoplastic; D006801:Humans; D007525:Isoelectric Focusing / Q000379:methods*; D013058:Mass Spectrometry / Q000379:methods*; D010455:Peptides / Q000737:chemistry; D040901:Proteomics / Q000379:methods*; D015203:Reproducibility of Results; D014357:Trypsin / Q000737:chemistry
chemical_list: D015415:Biomarkers; D002412:Cations; D010455:Peptides; D014357:Trypsin